R help - Oct 2007 - Problem with .libPaths & Rterm.exe (under Vista)

Dear list,

I?m using R embedded in another program (coded in tcl/tk) under Windows 
Vista. In this context I don?t launch Rgui.exe but rather Rtem.exe.


Now I have a problem finding libraries not specifically installed as 
administrator (and which are not in the path ?program files? but in 
Contacts\Documents of the current user). To be precise, the user 
launching my tcl/tk program can?t find the libraries he previously 
installed locally (as Vista does by default when not launched 
specifically with administrator rights).

However, when (manually) launching Rterm.exe directly (or R.exe) the 
command .libPaths() returns correctly 2 locations (the personal local 
library and the ?common? one in ?program files?) as it does with RGui.exe .

Does anyone have an idea how or why I can?t see the location of the 
additional libraries ?

Could it be a problem with the attributes of : Rterm.exe --vanilla -q < 
myRcode.r

(Note that I had no difficulties with these attributes calling R under 
Win XP or Linux, but never faced the problem of multiple locations for 
libraries.)


please find below the code form *(a)* launching : Rterm.exe ?vanilla ?q 
< myRcode.r (where ?local? libs are *NOT found*) :**
>  .libPaths()
"C://PROGRA~1/R/R-26~1.0/library"
>  require(affy)
Le chargement a n?cessit? le package : affy

Warning messages:

1: In library(package, lib.loc = lib.loc, character.only = TRUE, 
logical.return = TRUE, :

aucun package nomm? 'affy' n'est trouv?

 > # this translates into "no package called "affy" was
found"
>  sessionInfo()
R version 2.6.0 (2007-10-03)

i386-pc-mingw32

locale:

LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERattached
base packages:

[1] stats graphics grDevices utils datasets methods base




and the code from (b) manually launching : Rterm.exe (where ?local? libs 
are found OK) :
>  .libPaths()
[1] "C:\\Users\\wr\\Contacts\\Documents/R/win-library/2.6"

[2] "C:/PROGRA~1/R/R-26~1.0/library"
>
>require(affy) # was NOT installed in : program files/...
Le chargement a n?cessit? le package : affy

Le chargement a n?cessit? le package : Biobase

Le chargement a n?cessit? le package : tools

Welcome to Bioconductor

Vignettes contain introductory material. To view, type

'openVignette()'. To cite Bioconductor, see

'citation("Biobase")' and for packages
'citation(pkgname)'.

Le chargement a n?cessit? le package : affyio

Le chargement a n?cessit? le package : preprocessCore
>
>  sessionInfo()
R version 2.6.0 (2007-10-03)

i386-pc-mingw32

locale:

LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252

attached base packages:

[1] stats graphics grDevices utils datasets methods base

As you can see only a single path is found, which is the default 
collection of libraries in the path of the R installation itself.

Does anyone have an idea how I could identify the libPath for a given 
user and by which argument added to R.exe I could allow accessing these 
libraries, too ?

Thanks? in advance,
Wolfgang Raffelsberger


. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
. . .

Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et G?nomique Int?gratives
IGBMC
1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
Tel (+33) 388 65 3300 Fax (+33) 388 65 3276
wolfgang.raffelsberger at igbmc.u-strasbg.fr

On Thu, 4 Oct 2007, Wolfgang Raffelsberger wrote:
> Dear list,
>
> I?m using R embedded in another program (coded in tcl/tk) under Windows
> Vista. In this context I don?t launch Rgui.exe but rather Rtem.exe.
>
>
> Now I have a problem finding libraries not specifically installed as
> administrator (and which are not in the path ?program files? but in
> Contacts\Documents of the current user). To be precise, the user
> launching my tcl/tk program can?t find the libraries he previously
> installed locally (as Vista does by default when not launched
> specifically with administrator rights).
>
> However, when (manually) launching Rterm.exe directly (or R.exe) the
> command .libPaths() returns correctly 2 locations (the personal local
> library and the ?common? one in ?program files?) as it does with RGui.exe .
>
> Does anyone have an idea how or why I can?t see the location of the
> additional libraries ?
You mean the additional library what contains packages?  It really does 
help to get your terminology straight here.

What libraries are on .libPaths() is controlled by environment variables, 
so debugging those will be the key.  This is all explained on the help 
page for .libPaths.

> Could it be a problem with the attributes of : Rterm.exe --vanilla -q <
> myRcode.r
Yes, it could.  Look up what --vanilla does in ?Startup: it skips places 
where the environment variables are usually set.
>
> (Note that I had no difficulties with these attributes calling R under
> Win XP or Linux, but never faced the problem of multiple locations for
> libraries.)
>
>
> please find below the code form *(a)* launching : Rterm.exe ?vanilla ?q
> < myRcode.r (where ?local? libs are *NOT found*) :**
>
>>  .libPaths()
>
> "C://PROGRA~1/R/R-26~1.0/library"
>
>>  require(affy)
>
> Le chargement a n?cessit? le package : affy
>
> Warning messages:
>
> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE, :
>
> aucun package nomm? 'affy' n'est trouv?
>
> > # this translates into "no package called "affy" was
found"
>
>>  sessionInfo()
>
> R version 2.6.0 (2007-10-03)
>
> i386-pc-mingw32
>
> locale:
>
>
LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERattached
> base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
>
>
>
> and the code from (b) manually launching : Rterm.exe (where ?local? libs
> are found OK) :
>
>>  .libPaths()
>
> [1] "C:\\Users\\wr\\Contacts\\Documents/R/win-library/2.6"
>
> [2] "C:/PROGRA~1/R/R-26~1.0/library"
>
>>
>
>> require(affy) # was NOT installed in : program files/...
>
> Le chargement a n?cessit? le package : affy
>
> Le chargement a n?cessit? le package : Biobase
>
> Le chargement a n?cessit? le package : tools
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
>
> 'openVignette()'. To cite Bioconductor, see
>
> 'citation("Biobase")' and for packages
'citation(pkgname)'.
>
> Le chargement a n?cessit? le package : affyio
>
> Le chargement a n?cessit? le package : preprocessCore
>
>>
>
>>  sessionInfo()
>
> R version 2.6.0 (2007-10-03)
>
> i386-pc-mingw32
>
> locale:
>
>
LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252
>
> attached base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
> As you can see only a single path is found, which is the default
> collection of libraries in the path of the R installation itself.
>
> Does anyone have an idea how I could identify the libPath for a given
> user and by which argument added to R.exe I could allow accessing these
> libraries, too ?
>
> Thanks? in advance,
> Wolfgang Raffelsberger
>
>
> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
> . . .
>
> Wolfgang Raffelsberger, PhD
> Laboratoire de BioInformatique et G?nomique Int?gratives
> IGBMC
> 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
> Tel (+33) 388 65 3300 Fax (+33) 388 65 3276
> wolfgang.raffelsberger at igbmc.u-strasbg.fr
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595